"We grieve together for every mother, father, sister and brother, son and daughter who was stolen from us at the twin towers, at the Pentagon and here in this Pennsylvania field", he continued.
"This memorial is now a message to the world", he said.
Shanksville, the site where a hijacked plane crashed after passengers fought against terrorists who wanted to steer the flight to Washington, unveiled a new memorial for the 40 people who died.
"This field is now a monument to American defiance", Trump said, calling it "a message to the world: America will never, ever submit to tyranny".
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"While many of us remember that day like it was yesterday, a growing number of Americans have no living memory of what happened here".
On Tuesday, Trump marked the anniversary of the attacks by tweeting, "17 years since September 11th!"
Relatives of victims read out the names of the dead, and moments of silence were observed at 08:46 and 09:03 to mark the times when passenger jets struck the two skyscrapers.
The history of flight 93, who was to perform the liaison Newark-San Francisco, has given rise to several films, including "Flight 93" by Paul Greengrass.
Almost two decades after the deadliest foreign attack on United States soil, which killed almost 3,000 people, the Trumps traveled to Shanksville, Pennsylvania, to remember the fallen. Almost 3,000 people died in the attacks.
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All 59 passengers and crew aboard the flight were killed, along with another 125 personnel working in the Pentagon.
'(We) share their story and commemorate their incredible valor.' He also condemned the attackers, branding them 'evil men bent on terror and conquest'.
Mr Trump was accompanied by the First lady Melania, for this moment of national unity should offer him a temporary respite in the middle of a sequence to be particularly eventful.
"Even though I never met you", Isabella Del Corral said of her slain grandfather, Joseph Piskadlo, "I'll never forget you".
At the Pentagon, Vice-President Mike Pence recalled the heroism of service members and civilians who repeatedly went back into the Pentagon to rescue survivors.
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In addition to those killed on September 11, thousands of first responders, construction workers, and residents have since developed illnesses, many of them terminal, as a result of inhaling toxic fumes.